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Literature DB >> 28224794

1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations.

Leela S Dodda¹, Jonah Z Vilseck¹, Julian Tirado-Rives¹, William L Jorgensen¹.

Abstract

The quality of the 1.14*CM1A and 1.20*CM5 charge models was evaluated for calculations of free energies of hydration. For a set of 426 neutral molecules, 1.14*CM1A and 1.20*CM5 yield MADs of 1.26 and 1.21 kcal/mol, respectively. The 1.14*CM1A charges, which can be readily obtained for large systems, exhibit large deviations only for a subset of functional groups. The results for these cases were systematically improved using localized bond-charge corrections (LBCC) by which offsetting adjustments are made to the partial charges for atoms in specified bond types. Only 19 LBCCs were needed to yield 1.14*CM1A-LBCC charges that reduce the errors for the 426 ΔGhyd values to only 0.61 kcal/mol. The modified charge method was also tested in computation of heats of vaporization and densities for pure organic liquids, yielding average errors of 1.40 kcal/mol and 0.024 g/cm3, similar to those for 1.14*CM1A.

Entities: Chemical Disease Species

Mesh：

Substances：
Water

Year: 2017 PMID： 28224794 PMCID： PMC5813481 DOI： 10.1021/acs.jpcb.7b00272

Source DB: PubMed Journal: J Phys Chem B ISSN： 1520-5207 Impact factor: 2.991

29 in total

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Authors: Araz Jakalian; David B Jack; Christopher I Bayly
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2. Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP.

Authors: Jason D Thompson; Christopher J Cramer; Donald G Truhlar
Journal: J Comput Chem Date: 2003-08 Impact factor: 3.376

3. Accuracy of free energies of hydration using CM1 and CM3 atomic charges.

Authors: Marina Udier-Blagović; Patricia Morales De Tirado; Shoshannah A Pearlman; William L Jorgensen
Journal: J Comput Chem Date: 2004-08 Impact factor: 3.376

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Review 6. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

Authors: William L Jorgensen; Julian Tirado-Rives
Journal: J Comput Chem Date: 2005-12 Impact factor: 3.376

7. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

Authors: David L Mobley; Elise Dumont; John D Chodera; Ken A Dill
Journal: J Phys Chem B Date: 2007-02-10 Impact factor: 2.991

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Journal: J Phys Chem B Date: 2013-02-18 Impact factor: 2.991

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Journal: J Phys Chem B Date: 2019-01-03 Impact factor: 2.991

Review 2. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

Authors: A T Hagler
Journal: J Comput Aided Mol Des Date: 2018-11-30 Impact factor: 3.686

1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations.

1. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.

2. Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP.

3. Accuracy of free energies of hydration using CM1 and CM3 atomic charges.

4. Development and testing of a general amber force field.

5. Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases.

Review 6. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

7. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

8. Derivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization.

9. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

10. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

1. Unbinding Dynamics of Non-Nucleoside Inhibitors from HIV-1 Reverse Transcriptase.

Review 2. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.

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